[Bioperl-l] Bio_Tools_Run_RemoteBlast error: 500 Can't connect to www.ncbi.nlm.nih.gov:80

Alicia Amadoz Alicia.Amadoz at uv.es
Thu Jul 17 05:17:16 EDT 2008


Hi,

I am installing my bioperl script into a new server and I have an error that I don't know how 
to solve. Once I have launched my script at the new server, it appears a file named "delete" 
that has the following error:

-------------------- WARNING ---------------------
MSG: req was POST http://www.ncbi.nlm.nih.gov/blast/Blast.cgi
User-Agent: bioperl-Bio_Tools_Run_RemoteBlast/1.005002102
Content-Length: 610
Content-Type: application/x-www-form-urlencoded

DATABASE=nr&QUERY=%3Ee3768n+%0Aggtgcccactggggagtcctagcgggcatagcgtatttctccatggtg
gggaactgggcgaaggtcctgctagtgctgttgttgtttgccggcgtcgatgcggaaacctacatcaccggg
ggggccgtcgccaaggccgcgcttggattcactgggtttttcacttcgggccccaagcaggacatccagctaatcaactccaacgg
cagttggcacatcaatcgtactgccttgaactgtaatgcgagcctcgaaaccggctggatagcgg
ggctcctctatcacaacagattcaactcttcaggctgccccgagaggatggccagctgtagacccctcgccgacttcgaccagggct
ggggccctatcagctacgccaacggaagcggccccgatcaccgcccc&COMPOSITION_BASE
D_STATISTICS=off&EXPECT=10&SERVICE=plain&FORMAT_OBJECT=Alignment&ALIGNMENTS=
Pairwise&CMD=Put&FILTER=m&DESCRIPTIONS=100&PROGRAM=blastn&ALIGNMENT_VIEW=P
a
irwise

<HTML>
<HEAD><TITLE>An Error Occurred</TITLE></HEAD>
<BODY>
<H1>An Error Occurred</H1>
500 Can't connect to www.ncbi.nlm.nih.gov:80 (Bad hostname 'www.ncbi.nlm.nih.gov')
</BODY>
</HTML>

---------------------------------------------------

My script works ok in my current machine, a fedora 5 with bioperl 1.4 installed through 
cpan. The new server is a fedora 8 and we installed bioperl and bioperl run 1.5.2 through 
yumex installer. Both machines have perl 5.8.8 installed.

Any idea of how to solve this error?? Thank you very much in advance.

Alicia

Here you are a part of my script:

#!/usr/bin/perl 

use Bio::Seq;
use Bio::SeqIO;
use Bio::SearchIO;
use Bio::DB::GenBank;
use Bio::Tools::Run::RemoteBlast;
use POSIX;
use strict;
use File::Copy;

# Blast using RemoteBlast
# get php variables

my $query_filename = $ARGV[0]; 
my $query_filepath = $ARGV[1]; 
my $database = $ARGV[2]; 
my $program = $ARGV[3]; 
my $ALIGNMENTS = $ARGV[5]; 
my $ALIGNMENT_VIEW = $ARGV[5];
my $DESCRIPTIONS = $ARGV[6];
my $EXPECT = $ARGV[7]; 
# maybe "novar" variables
my $FILTER_1 = $ARGV[8]; 
my $FILTER_2 = $ARGV[9];
my $LCASE_MASK = $ARGV[10]; 
my $MEGABLAST = $ARGV[11]; 
my $UNGAPPED_ALIGNMENT = $ARGV[12]; 
my $user_name = $ARGV[13]; 
my $perlfunc_path = $ARGV[14]; 
my $input = $ARGV[15]; 
my $format = $ARGV[16];  

my $ENTREZ_QUERY = $ARGV[17];

my @params = ('-prog' => $program, '-data' => $database, '-expect' => $EXPECT, '-
readmethod' => 'SearchIO');

my $remote = Bio::Tools::Run::RemoteBlast->new(@params);
# change query parameters
$Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENTS'} = $ALIGNMENTS;
$Bio::Tools::Run::RemoteBlast::HEADER{'ALIGNMENT_VIEW'} = $ALIGNMENT_VIEW;
$Bio::Tools::Run::RemoteBlast::HEADER{'DESCRIPTIONS'} = $DESCRIPTIONS;

..








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